Abstract: The present invention is directed to in situ methods for providing a definitive haplotype of a subject. The haplotype information generated by the methods described herein is more accurate than that provided by prior art methods that only give an inferred haplotype. Accordingly, in one aspect the present invention provides an in situ method for obtaining genetic information for a polyploid subject, the method including the steps of obtaining a biological sample from the subject, the sample containing: (i) at least one paternally-derived DNA molecule, and/or (ii) at least one maternally-derived DNA molecule, analyzing any one or more of the paternally- or maternally-derived DNA molecules for nucleotide sequence information, wherein the step of analyzing determines whether any two DNA markers are present in cis on one chromosome, or in trans across two sister chromosomes.

Abstract: The present invention provides a method for identifying a set of target nucleotide sequences capable of identifying a member of a group of related nucleotide sequences, the method comprising the step of dividing the nucleotide sequence of each member of the group into a plurality of subsequences, wherein at least two of the subsequences overlap. The method is useful in generating probe sets capable of assigning alleles at HLA or KIR loci.

Abstract: The present invention provides a method for identifying a microarray probe set capable of identifying a member of a group of related nucleotide sequences, the method comprising the steps of providing a candidate probe set comprising at least one probe capable of differentially hybridizing to two or more members of the group of related nucleotide sequences, testing reactivity of the probe set against two or more members of the group of related nucleotide sequences, and observing the degree of difference in the patterns of reactivity of the probe set for the two or more members of the group of related nucleotide sequences.

Abstract: The present invention provides methods for obtaining epigenetic information for a polyploid subject, the method including the steps of obtaining a biological sample from the subject, the sample containing: (i) at least one paternally-derived DNA molecule and/or associated protein and/or, (ii) at least one maternally-derived DNA molecule and/or associated protein, analyzing any one or more of the paternally- or maternally-derived DNA molecules or associated proteins for the presence or absence of modifications, wherein the step of analyzing determines whether any two modifications are present in cis on one chromosome, or in trans across two sister chromosomes.

Abstract: The present invention provides a method for identifying a set of target nucleotide sequences capable of identifying a member of a group of related nucleotide sequences, the method comprising the step of dividing the nucleotide sequence of each member of the group into a plurality of subsequences, wherein at least two of the subsequences overlap. The method is useful in generating probe sets capable of assigning alleles at HLA or KIR loci.

Abstract: The present invention is directed to in situ methods for providing a definitive haplotype of a subject. The haplotype information generated by the methods described herein is more accurate than that provided by prior art methods that only give an inferred haplotype. Accordingly, in one aspect the present invention provides an in situ method for obtaining genetic information for a polyploid subject, the method including the steps of obtaining a biological sample from the subject, the sample containing: (i) at least one paternally-derived DNA molecule, and/or (ii) at least one maternally-derived DNA molecule, analyzing any one or more of the paternally- or maternally-derived DNA molecules for nucleotide sequence information, wherein the step of analyzing determines whether any two DNA markers are present in cis on one chromosome, or in trans across two sister chromosomes.

Abstract: The present invention is directed to methods for providing a definitive haplotype of a subject. The haplotype information generated by the methods described herein is more accurate than that provided by prior art methods that only give an inferred haplotype. Accordingly, in one aspect the present invention provides a method for determining a definitive haplotype of a subject the method including the steps of providing a substantially isolated haploid element from the subject, and obtaining nucleotide sequence information from the haploid element. Applicants propose that the use of a substantially isolated haploid element eliminates the problem of incorrect or misleading inferences concerning the phase of two or more loci within a haplotype, and allows for revelation of two or more participatory genes within a haplotype, uncomplicated by differences in modes of inheritance.

Abstract: The present invention provides a method for identifying a set of target nucleotide sequences capable of identifying a member of a group of related nucleotide sequences, the method comprising the step of dividing the nucleotide sequence of each member of the group into a plurality of subsequences, wherein at least two of the subsequences overlap. The method is useful in generating probe sets capable of assigning alleles at HLA or KIR loci.